Tuesday, March 31, 2009

First, it is really really surprising that they are so low on females here (41 men, 9 women by my count). Given that this is for early career scientists and that women have on average sometime more challenges in the early career than men, it would have been nice to see this the other way around.

That being said, they did pick some good people in this list (shocking, I know). Here are a few I want to highlight as they are related to things I tend to write about here:Rob Knight, at U. Colorado at Boulder who has been developing computational methods to study microbial diversity and has developed lots of cool methods.Harmit Malik, FHCRC, who does some great stuff on genome evolution.Michael Laub, MIT who works on Caulobacter development.Martin Cohn, U. Florida who has done some very cool work on evolution of development in vertebrates.Neil Hunter UC Davis. UCD's first HHMI awardee. And a good one to pick. He does some cool work on recombination.Molly Przeworski, U. Chicago, who works on population genetics on a genome-wide scale.Aviv Regev, Broad Institute, who has done some interesting work on regulatory networks.

I love the idea of finding people not projects. Too bad there is not more of this type of thing from Federal Agencies. We would probably save money in the long run --- review people once every few years and give them some money to do work. Not that competitive grant programs should be eliminated, but funding people more would reduce the # of grant proposals and panels and would probably save $$ in the long run by allowing people to focus on doing work.

For those not in the now, Sean is a big supporter and proponent of Open Science and is now at the HHMI's Janelia Farm Campus. In addition to developing some smashing software and doing cool science, Sean was instrumental in my conversion to supporting Open Science so I pay attention to what he says. And there is some interesting material in this pub. The ending sums up a lot of what is in there:

More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

Basically, Sean is saying the Open Education is great in concept but that many Open Education resources need work for them to be effective. And that work can take a lot of money. So we need to find ways to get more money into the development of Open Education materials.

Saturday, March 28, 2009

Well, the Joint Genome Institute (JGI) Users Meeting is Over. For some rapid fire notes on the meeting see the FriendFeed room here. where Jason Stajich, Tom Sharpton and I (and occasionally a few others) took notes on the whole thing as it was happening.

So - what were the lessons learned? What were the main points? So - if you want to know what we were writing about - and don't want to read the notes (they are quite fun actually) how about a word cloud? Well, here is one, which I made by taking the notes, editing out some of the names and other non notes text, and then pasting them into TagCrowd.Com and I got this to the left here:

Not actually a bad representation of many of the topics.

But you know, this does not per se capture the big points, just the common points. So I guess if you want the key points, you have to think a bit. First, you have to realize this is a JGI focused meeting (which of course is the whole point of the meeting - it is the JGI User Meeting after all) and most of the people work with JGI in some way so it is a bit hard to see the forrest of genomics for the JGI trees. And here are my top lessons I got out of the meeting after trying to not get too biased by the JGI focus (note - I have an Adjunct Appt. at JGI and do lots of things through there so I am sure I cannot remove the JGI focus completely)

NextGen sequencing continues to open up new windows into biology.

Ecological and population genomics are truly the next big thing.

Related to the above point, one of the next revolutions is going to be in high throughput phenotyping --- after all, we cannot solve the genotype-phenotype problem when we only know the genotype.

Model / reference organisms are still in, but every single organism on the planet is now in play.

NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and to use it well.

Related to the above point, the NextNextGen (e.g., Pacific Biosciences) seems to be barreling along and almost ready for prime time. WTF are we going to do in terms of informatics then?

Following up on the above point- we desperately need a MASSIVE effort in the development of tools for "normal" biologists to make better use of massive sequence databases.

I am happy to report that just about everyone seems to be trying to use an evolutionary perspective as part of their work - especially in the selection of organisms for sequencing

I am sorry to report that many of the evolutionary "perspectives" are a bit off kilter.

Sequencing is definitely not over - it is just getting started.

People pushing the technology (e.g., George Church, Craig Venter) into new arenas definitely inspire the crowds.

If you study a plant or an animal and are not studying the microbes that live with them, you are missing something.

If you study ANY organism and are ignoring epigenetics you are behind the curve

Open Access journals like PLoS Biology and PLoS One and Open Science got some huge props at this meeting, for example, with Venter showing many PLoS related images, many others showing stuff from OA journals, George Church talking about Open Source sequencers and Open personal genomics, and many referring to Open genomics databases. Still some areas in need of improvement (e.g., not enough publishing in open access journals still) but the move in the direction of openness is great.

Genome Centers definitely each have their own flavors with JGI positioning itself well in the niches of Ecology, Evolution, and Energy.

Genome Centers are definitely going to have to reinvent themselves as the sequencing capacity for individual labs goes up and up with Illumina/Roche/ABI Solid continuing to spread. Bigger, better, faster, more is one way they can stay ahead of the curve.

Education and training did not get as much play during the talks as I would have hoped. I mentioned it a bit but I do not recall too many other mentions. Too bad as the real potential for the democritization of sequencing comes from people getting trained in how to generate and handle the data and how to at least think about it even if they do not use it directly.

Organismal biology is still desperately important in all of this work - if you know a lot about the organism as a whole then you already are a systems biologist.

Genomic characterization of entire multi-organism systems is on the rise and this is not just microbiota stuff but also things like host-pathogen interactions and symbioses and so on.

Reading DNA is being used in every which way imaginable. Next up - writing DNA.

Wednesday, March 25, 2009

Well, I am at the JGI (Joint Genome Institute) User Meeting - and I am going to try and do some live blogging right here. I am going to do it differently than I have previously and do things in the comments not in the main page here. If it works, great. If not I might switch to FriendFeed. So check out the comments for new updates ....

So - see the comments for this posting but also see FriendFeed where Jason Stajich and I posted many comments. Here are some links:

Tuesday, March 24, 2009

"The Extreme Ice Survey is the most wide-ranging glacier study ever conducted using ground-based, real-time photography. EIS uses time-lapse photography, conventional photography, and video to document the rapid changes now occuring on the Earth's glacial ice. The EIS team has installed 27 time-lapse cameras at 15 sites in Greenland, Iceland, Alaska, and the Rocky Mountains. EIS supplements this ongoing record with annual repeat photography in Iceland, the Alps, and Bolivia."

Went to a dinner last night that was in honor of Sean Carroll who is visiting Davis as part of the "Storer" lecture series. It was the first time I have met Sean -- but I have followed him and his writing extensively. I already found him to be one of the best of the best in science and in explaining evolution. I really liked "The Making of the Fittest" and now he has a new one --- which I have not read but it sounds great. It is called "Remarkable Creatures: Epic Adventures in the Search for Origin of Species". He was also quite entertaining at the dinner and handled being peppered with questions very well. Alas I have to miss his talk today since I am at the Joint Genome Institute for a discussion about metagenomic sequencing of samples from Yellowstone National Park.

Anyway - just wanted to write something because I found my brief interaction with him inspiring. It makes me want to do more engagement of the public on evolution than I have been doing (I do some but he inspired me to do more). I also got to meet some of the Storer family who are the people who gave the money to set up the Storer lecture series. It was also inspiring to talk to them - and good to see people giving money to spread knowledge in the life sciences. It was overall a good day for me after being sick for a month and then spending two weeks writing grants ...

Sunday, March 22, 2009

Hey - that looks like good old Charlie D. in the room of the lead character in Fox's Lie to Me. Seems likely that it is, given that the show is advised by Paul Ekman from UCSF who is into Darwin. And of course, it really looks like some of the classic pics of Charlie. Good to see Fox TV is not too sold by the lame anti-evolution rhetoric sometimes spouted on Fox News.

*Admission to this class is by application only; Scholarship support is available!*

This course offers students opportunities to use state-of-the-art genomic methods to address questions about the structure and function of microbial communities.Our field site will be the Long Term Ecological Research Site at KBS. The nucleic acid based data generated during the course will be integrated with the expansive data set from the KBS LTER, which includes measurements of the flux of greenhouse gases.

The ultimate goal of the course is to uncover relationships between changes in microbial communities and ecosystem functions.

Morning lectures will address pertinent ecological theories and principles underlying experiments that will be conducting during the afternoon. The afternoon laboratory sessions will be focused on molecular methods, including generation purification of DNA from soil, PCR amplification and construction of clone libraries, and quantitative PCR. This is an intensive 2-week course modeled after the longer and internationally acclaimed MBL Microbial Diversity Course that Dr. Schmidt directs. 3 Credits.

The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation ofthe US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/).

Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.

NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, toalignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests.

TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009.

INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible.

Wednesday, March 18, 2009

Posting some notices here I have been getting from various federal agencies ...

Important Notice 131, American Recovery and Reinvestment Act of 2009Available Formats: PDFType: Announcements and Notices Subtype: Important NoticesOrganization/Group: Office of Budget, Finance, and Award Management

National Science FoundationOffice of the DirectorArlington, VA 22230

March 18, 2009

Notice No. 131

IMPORTANT NOTICE TOPRESIDENTS OF UNIVERSITIES AND COLLEGESAND HEADS OF OTHER NATIONAL SCIENCE FOUNDATIONAWARDEE ORGANIZATIONS

Subject: American Recovery and Reinvestment Act of 2009

On February 17, 2009, President Obama signed the American Recovery and Reinvestment Act of 2009 (Recovery Act) into law. One of the principal purposes of the law is to “provide investments needed to increase economic efficiency by spurring technological advances in science and health”.[1] During the signing ceremony President Obama stated,

"Even beyond energy, from the National Institutes of Health to the National Science Foundation, this recovery act represents the biggest increase in basic research funding in the long history of America’s noble endeavor to better understand our world. Just as President Kennedy sparked an explosion of innovation when he set America’s sights on the moon, I hope this investment will ignite our imagination once more, spurring new discoveries and breakthroughs that will make our economy stronger, our nation more secure, and our planet safer for our children."[2]

In response to this landmark legislation, NSF has developed policies, procedures, and Frequently Asked Questions for use by the awardee community. These documents provide up-to-date information regarding NSF’s implementation of the Recovery Act, and are available at www.nsf.gov/recovery. The key elements of NSF’s implementation of the Recovery Act are highlighted below.

NSF Programs Receiving Recovery Act Funding

The Recovery Act supplements NSF fiscal year 2009 funding by $3.0 billion. NSF currently has many highly rated proposals that it has not been able to fund. For this reason, NSF is planning to use the majority of the $2 billion available in Research and Related Activities for proposals that are already in house and will be reviewed and/or awarded prior to September 30, 2009.

The Foundation also expects to expeditiously award funds as specified in the Recovery Act for: the Math and Science Partnership program (funded at $25 million); the Robert Noyce Teacher Scholarship Program (funded at $60 million); the Major Research Equipment and Facilities Construction Account (funded at $400 million); the Academic Research Infrastructure (ARI) program (funded at $200 million); and the Science Masters program, (funded at $15 million). Solicitations for these latter two programs will be posted this spring.

NSF will post a solicitation this spring for the Major Research Instrumentation Program (MRI) in order to make a sufficient number of awards to utilize the $300 million provided in the legislation. The Foundation currently anticipates that no other solicitations will be posted that are solely in response to the Recovery Act.

Funding Prioritization

NSF will ensure that Recovery Act funds are awarded in a timely manner while maintaining its commitment to its established merit review processes.

All grants issued with Recovery Act funds will be standard grants with durations of up to 5 years. This approach will allow NSF to structure a sustainable portfolio.

Funding of new Principal Investigators and high-risk, high-return research will be top priorities.

With the exception of the MRI, ARI and Science Masters programs, the majority of proposals eligible for Recovery Act funding include those that are already in house and will be reviewed and/or awarded prior to September 30, 2009.

NSF also will consider proposals declined on or after October 1, 2008. The reversal of the decision to decline must be based on both the high quality of the reviews received on the initial submission and the lack of available funding at the time the original decision was made. The cognizant program officer will contact the institution when a reversal is being considered by NSF. Specific procedural information regarding this new process is available on the NSF Recovery website.

Special Award Conditions

The Recovery Act mandates a significant level of transparency and accountability. The law and implementing guidance identify specific award conditions for awards made with Recovery Act funding. Therefore, award notices will include special award conditions identifying the funding as coming from the Recovery Act, and indicate the specific awardee reporting responsibilities mandated by Section 1512 of the Recovery Act.

Given the goals of the Recovery Act, awardees will be informed that they are expected to expend funds in a timely manner on allowable award costs and that NSF will be monitoring awards for expenditures. If, after 12 months, no allowable expenditures have taken place, NSF may consider reducing or terminating the award and reallocating the funds.

Working in Partnership

NSF is honored by the recognition of the Foundation's role in stimulating the American economy with its inclusion in the Recovery Act. The law and implementing guidance issued by the Office of Management and Budget (OMB) set clear expectations for accountability and transparency from both Federal agencies and from recipients of Recovery Act funding.

The high expectations embodied in the Recovery Act acknowledge the contributions that NSF and its partners in the research and education community have made to the economy and welfare of the nation over the past six decades. This partnership is one of the nation’s greatest strengths, and we look forward to working with you as we continue to pursue the promise of science and engineering and meet the goals of the Recovery Act for securing the nation’s future.

Arden L. Bement, Jr.Director

[1] P.L. 111-5, Section 3 (a) (3). The full text of the American Recovery and Reinvestment Act of 2009 is available electronically at: http://frwebgate.access.gpo.gov/cgi-bin/getdoc.cgi?dbname=111_cong_bills&docid=f:h1enr.pdf[2] The full text of President Obama’s remarks at the signing ceremony is available at: http://www.whitehouse.gov/the_press_office/Remarks-by-the-President-and-Vice-President-at-Signing-of-the-American-Recovery-and-Reinvestment-Act/

All NSF official issuances can be found on Inside NSF at http://infoshare.nsf.gov.

If you need a paper copy of this issuance, contact the Supply Unit on P-1 at ext. 8134.

Friday, March 06, 2009

In case you are not aware, my brother (Michael Eisen) and Larry Lessig have been engaging in a public "debate" with John Conyers over Conyers' sponsorship of a bill to revoke the NIH policy on Open Access to publications. First the elder Eisen and Lessig wrote a posting:Is John Conyers Shilling for Special Interests? which they then followed up with John Conyers, It's Time to Speak Up. Now Conyers has written a reply:A Reply to Larry Lessig (which I note should have been titled A Reply to Eisen and Lessig, but that is for another day). Anyway it is worth reading them all and if I had not been sick for the last like 3-4 weeks I would write more but I have a million things to catch up on now that I have mostly gotten rid of nasty microbe #3.

Tuesday, March 03, 2009

Well, the human microbiome is all over the news recently thanks to a new paper on the diversity and biogeography of microbes in human saliva. The paper "Global diversity in the human salivary microbiome Global diversity in the human salivary microbiome" was by Mark Stoneking's lab and is in press in Genome Research (I am following my brother's trend and not putting a link here since the paper in non Open Access). In the paper Nasidze et al report on the use of PCR and sequencing of the rRNA genes from bacteria in human saliva from 120 people. They compare and contrast the samples (14000 sequences in total) and make some conclusions about the connection between bacterial diversity and genetic biogeography of the people from which the samples came.

Get ready for much more in the next few years about microbes in and on us (see my discussion of this previously).

My only complaint is that I and Stoneking and many others have unfortunately made a mess of the terminology. The "microbiome" was originally used to refer to the collection of the genomes of the microbes in a particular ecosystem. And the terms "microbiota" was used to refer to the actual organisms. Since Stoneking et al did not survey the genomes, they surveyed rRNA (which really at best tells you about what types of organisms are present) then they should have used microbiota riight? (And if they had I would not have been searching for the genomics component of their work).

Not so fast, even the person who coined the term microbiome (Josh Lederberg) who originally seemed to use it to refer to all the genomes of the microbes also used the term ambiguously (e.g., in one paper he sad "the microbiome flora" meaning I guess the microbiota.

I note, everyone seems to cite A paper by Lederberg called "Infectious History" in Science (Science 14 April 2000:) as the place he used microbiome but I cannot find the term there. I did however find the term in a paper in 2001 by Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118).

The Nobel laureate Joshua Lederberg has suggested using the term"microbiome" to describe the collective genome of our indigenousmicrobes (microflora), the idea being that a comprehensive geneticview of Homo sapiens as a life-form should include the genes inour microbiome (4).

And reference 4 is "Personal communication"

Anyway, others have taken the term microbiome and run with it because it does conjure up to many "microbial biome" which could be used to refer to all the microbes in a system. I prefer the original definitions with microbiota being the organisms and microbiome being the collective genomes of all the organisms.

I have been as guilty as others in mixing up the terms but in the future I plan to push for "microbiome" to be an omics word and not a biome word and for microbiota to be the biome word. That way if you skim a paper or title you might be able to better guess what it is about.

Monday, March 02, 2009

There really is no better advocate for Science these days than Harold Varmus. He balances politics and science incredibly well and also simultaneously advocates for applied and basic science as well as access to scientific information. Here is the clip of his latest interview on The Daily Show.

To me, science is about the spread of ideas and knowledge. And as long as I get credit for my ideas and my writing, I am more than happy for people to run with them. I feel the same way about my blog. Thus I was happy when a blog called The Reef Tank said they wanted to include more science about marine biology there and wanted to cross post some of my marine focused postings. And they have done the first one here. All the power to them for wanting to include more science there and happy they are giving my postings another life ...

Well, it has finally happened. And not sure how. But PDFs of all my papers, which I have posted on my MAC.COM (or now known as ME.COM) homepage are finally showing up on Google Scholar. If you go to Google Scholar and type Eisen JA into the window and then look for PDFs for each of the papers some of the files on my .MAC site show up.

When I originally discovered a few months ago that none of my PDFs from this site where showing up on Google Scholar I dug around and discovered in Google's Faqs that it helps to have links to the PDFs of papers. This seemed strange since I had links from my blog and that is run by Google now so it was weird that those did not help. But I added some more links here and there and presto, now the links to the PDFs are showing up inside Google Scholar results.

Mind you, not all of the PDFs have shown up yet and I have no clue why some did and some did not, but this is part of my continuing effort to free up my past publications. Good start. Not done yet, but getting there.

Just a quick note here. For anyone interested in Open Access and science policy in general, Harold Varmus, Nobel Laureate and CoFounder of PLoS, will be on the Daily Show tonight to promote his new book The Art and Politics of Science. Now when are they going to have my brother on the show? He was a CoFounder of PLoS. So what if he does not have a Nobel and never ran NIH. He has won some cool awards here and there, is an HHMI Investigator, and more importantly, he has a blog and Varmus does not. Doesn't that count for something?